HorA Server Transitive Detail

Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets. J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity. Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu


Query: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.100 --> Intermediate <-- 1.253 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1j5pa4) through the intermediate protein (d1l7da1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1l7da1 Nicotinamide nucleotide transhydrogenase dI componentNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β
Hit d1j5pa4 Hypothetical protein TM1643NAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β

Supporting Alignments

Query <-- 1.100 --> Intermediate
DALI alignment (Z-score: 5.1 Raw score:345.40) query 1 ---------------GMEN----------KKMNLLLfsgdydkALASLIIANAAREMEIE 35 :::: ::::::: ::::::::::::::::: d1l7da1 1 agyravidgayefarAFPMmmtaagtvppARVLVFG------vGVAGLQAIATAKRLGAV 54 query 36 VTIFCafwgLLLLrdpekasqedkslyeqafssltpreaeelplskmnlggigkkmllem 95 ::::: :::: d1l7da1 55 VMATD----VRAA----------------------------------------------- 63 query 96 mkeekapklsdllSGARKKEVKFYAXQLsveimgfkkeelfpevqimDVKEYLKNALESD 155 ::::::::::::::: ::::::::::::: d1l7da1 64 -----------tkEQVESLGGKFITVKK-------------------QAEAVLKELVKTD 93 query 156 LQLFI------------------------------------------------------- 160 ::::: d1l7da1 94 IAITTalipgkpapvliteemvtkmkpgsviidlaveaggncplsepgkivvkhgvkivg 153 query 161 ------- 161 d1l7da1 154 htnvpsr 160 FAST alignment (Normalized score: 3.90 Raw score:624.80) query 1 GME----------------------------NKKMNLLLFSGDYDK---ALASLIIANAA 29 :::::: ::::::::::: d1l7da1 1 ---AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLV---------FGVGVAGLQAIATA 48 query 30 REMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGK 89 :::::::::: d1l7da1 49 KRLGAVVMAT-------------------------------------------------- 58 query 90 KMLLEMMKEEKAPKLSD-----LLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIM-- 142 :::::::::::::: d1l7da1 59 -----------------DVRAATKEQVESLGGKFIT----------------------VK 79 query 143 -DVKEYLKNALESDLQLFI----------------------------------------- 160 :::::::::::::::: d1l7da1 80 KQAEAVLKELVKTDIAI--TTALIPGKPAPVLITEEMVTKMKPGSVIIDLAVEAGGNCPL 137 query 161 ----------------------- 161 d1l7da1 138 SEPGKIVVKHGVKIVGHTNVPSR 160 TMalign alignment (TM-score: 0.23 Raw score:37.44) query 1 ------------------------------GMENKKMNLLLFSGDYDKALASLIIANAAR 30 d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPA------------------------------ 30 query 31 EMEIEVTIFCAFWGLLLLRDPEK--AS--QEDKSLYEQAFSSLTPREAE----------- 75 :: ::: ::::: :: :::::: : :: :: ::: d1l7da1 31 -----------RV-LVF-GVGVAGLQAIATAKRLG-A--VV--MA-TDVRAATKEQVESL 71 query 76 ---ELPL-SK-----------------MNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKK 114 :::: :: ::::::: d1l7da1 72 GGKFITVKKQAEAVLKELVKTDIAITT--------------------------ALIPGKP 105 query 115 EVKFYA---X----QLSVEIMGFKKEELFPE---V----Q----IMDVKEY--------- 147 :::::: : :::: : : :::: : : ::::::: d1l7da1 106 APVLITEEMVTKMKPGSV----I-I--DLAVEAGGNCPLSEPGKIVVKHGVKIVGHTNVP 158 query 148 --LKNALESDLQLFI 160 d1l7da1 159 SR------------- 160 HHsearch alignment (Probability: 0.09 E-value:0.01) query 21 ASLIIANAAREMEIEVTIF 39 ::::::::::::::::::: d1l7da1 40 AGLQAIATAKRLGAVVMAT 58
Intermediate <-- 1.253 --> Hit
DALI alignment (Z-score: 8.8 Raw score:531.30) d1l7da1 1 agyravidgayefaraFPmmmtaagtvppARVLVFGVGVAGLQAIATAkrLGAVVMATDV 60 :: ::::::::::::::::::: :::::::::: d1j5pa4 1 ----------------HH-----------MTVLIIGMGNIGKKLVELG--NFEKIYAYDR 31 d1l7da1 61 RAATKeqvesLGGKFITvkkqaeAVLKElVKTDIAITTALipgkpAPVL--ITEEMVTKM 118 ::::: ::::::: ::::: ::::::::::: :::: ::::::::: d1j5pa4 32 ISKDI-----PGVVRLD------EFQVP-SDVSTVVECAS-----PEAVkeYSLQILKNP 74 d1l7da1 119 kpgSVIIDLAVEAG-gncplsepgkivvKHGVKIVGHTnVPSR----------------- 160 ::::::::::: :::::::::: :::: d1j5pa4 75 ---VNYIIISTSAFadevfrerffselkNSPARVFFPS-GSMLtvysilrtlrnleskii 130 d1l7da1 161 -- 161 d1j5pa4 131 fg 132 FAST alignment (Normalized score: 5.48 Raw score:797.00) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLG---AVVMA 57 :::::::::::::::::::: ::::: d1j5pa4 1 ---------------------------HHMTVLIIGMGNIGKKLVEL-----GNFEKIYA 28 d1l7da1 58 TDVRAATKEQVE---SLGGKFITVKKQAEAVLKE------LVKTDIAITTALIPGKPAPV 108 :::: :::::: :::::::::: d1j5pa4 29 YDRI--------SKDIPGVVR-------------LDEFQVPSDVSTVVEC---------- 57 d1l7da1 109 LI--------TEEMVTKMKPGSVIIDLAVEAGGNCPLSEPGKIVVK-------------- 146 ::::::: ::::::::::: d1j5pa4 58 --ASPEAVKEYSLQILK--NPVNYIIISTS----------------AFADEVFRERFFSE 97 d1l7da1 147 ---HGVKIVGHTNVPSR------------------------ 160 :::::::: d1j5pa4 98 LKNSPARVFFP------SGSMLTVYSILRTLRNLESKIIFG 132 TMalign alignment (TM-score: 0.54 Raw score:86.26) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAVVMATDV 60 :: ::::::::::::::::::: :::::::::: d1j5pa4 1 ----------------HH-----------MTVLIIGMGNIGKKLVELG--NFEKIYAYDR 31 d1l7da1 61 RAATKEQVESLGGKFITVKKQAEAVLKELVKTDIAITTALIPGKPAP--VLITEEMVTKM 118 ::: : :: :::::: : :::: ::::::::::: :: ::::::::: : d1j5pa4 32 ISK--D-IP--GVVRLD---E---FQVP-SDVSTVVECAS-----PEAVKEYSLQILK-N 73 d1l7da1 119 KPGSVIIDLAVEAGG----NCP--LS--EPGKIVVKHGVKIVGHTNV--PS--R------ 160 : :::::::: ::: :: :: :::::::::::: : :: : d1j5pa4 74 P--VNYIIIST-SAFADEV-FRERFFSE-----LKNSPARVFFPS-GSMLTVYSILRTLR 123 d1l7da1 161 --------- 161 d1j5pa4 124 NLESKIIFG 132 HHsearch alignment (Probability: 0.91 E-value:0.00) d1l7da1 30 ARVLVFGVGVAGLQAIATAKRLGAVVMATDVRAATKEQVESLGGKFITVKKQAEAVLKEL 89 :::::::::::::::::::: :::::::::::::::::::: :::::: d1j5pa4 3 MTVLIIGMGNIGKKLVELGN--FEKIYAYDRISKDIPGVVRL------------DEFQVP 48 d1l7da1 90 VKTDIAITTALIPGKPAPVLITEEMVTKMKPG 121 :::::::::: : ::::::::::::::: d1j5pa4 49 SDVSTVVECA--S----PEAVKEYSLQILKNP 74